Manual for SS-QRRK utility code

Manual for SS-QRRK utility code SS-QRRK: A Program for System-Specific Quantum Rice-Ramsperger-Kassel Theory Junwei Lucas Bao and Donald G. Truhlar Department of Chemistry Chemical Theory Center, and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455 Program version: 2017 Program version date: Aug 01, 2017 Manual version date: Aug 02, 2017 Copyright 2017

2 Table of contents 1. Introduction and recommended citations... 3 2. Theoretical background of SS-QRRK... 4 2.1 Hinshelwood Lindemann mechanism for unimolecular reactions... 4 2.2 Chemical activation mechanism for bimolecular association... 9 2.3 Energy transfer parameters... 11 3. Fitting high-pressure-limit rate constants... 13 4. Description of input... 14 4.1 Unimolecular reaction... 14 4.2 Bimolecular association... 19 4.3 Bimolecular reaction with an intermediate... 21 4.4 Other input files... 25 5. Test runs... 26

3 1. Introduction and recommended citations This is a manual for the SS-QRRK utility code, which is included in the Polyrate program (in the directory polyrate17/util/ss-qrrk/). The SS-QRRK utility code is a program for calculating pressure-dependent rate constants using variational transition state theory. To execute the code, put input files with the.exe file in a working directory, and then type./falloff.exe &. Recommend citations (Please cite the following two papers for SS-QRRK): (1) Kinetics of Hydrogen Radical Reactions with Toluene by Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory, J. L. Bao, J. Zheng, and D. G. Truhlar, Journal of the American Chemical Society 138, 2690-2704 (2016). dx.doi.org/10.1021/jacs.5b11938 (2) Predicting Pressure-Dependent Unimolecular Rate Constants Using Variational Transition State Theory with Multidimensional Tunneling Combined with System-Specific Quantum RRK Theory: A Definitive Test for Fluoroform Dissociation, J. L. Bao, X. Zhang, and D. G. Truhlar, Physical Chemistry Chemical Physics 18, 16659-16670 (2016). dx.doi.org/10.1039/c6cp02765b For the citation of Polyrate program: (3) J. Zheng, J. L. Bao, R. Meana-Pañeda, S. Zhang, B. J. Lynch, J. C. Corchado, Y.-Y. Chuang, P. L. Fast, W.-P. Hu, Y.-P. Liu, G. C. Lynch, K. A. Nguyen, C. F. Jackels, A. Fernandez Ramos, B. A. Ellingson, V. S. Melissas, J. Villà, I. Rossi, E. L. Coitiño, J. Pu, T. V. Albu, A. Ratkiewicz, R. Steckler, B. C. Garrett, A. D. Isaacson, and D. G. Truhlar, POLYRATE version 2017, University of Minnesota, Minneapolis, 2017 See also for applying SS-QRRK for barrierless reactions: (4) Barrierless association of CF 2 and dissociation of C 2 F 4 by variational transition state theory and system-specific quantum Rice-Ramsperger-Kassel theory, J. L. Bao, X. Zhang, and D. G. Truhlar, Proceedings of the National Academy of Sciences, U.S.A., 113, 13606 13611 (2016). dx.doi.org/10.1073/pnas.1616208113

4 2. Theoretical background of SS-QRRK System-specific quantum RRK (SS-QRRK) theory is an efficient way to incorporate variational effects, multidimensional quantum mechanical tunneling, and multi-structural torsional anharmonicity into the calculation of pressure-dependent rate constants in the falloff region of chemical reactions. Recall that unimolecular reactions may have pressure-dependent rate constants because only in the high-pressure limit can the usual assumption of thermally equilibrated states in the reactant be justified. Furthermore, association reactions (whose reverse reactions are unimolecular) may also be pressure dependent because the newly formed states of the associated species (which can be an intermediate or a product) may redissociate before they are equilibrated. SS-QRRK theory uses information obtained from the high-pressure-limit canonical rate constants (i.e., the thermal equilibrium rate constants) to compute the microcanonical rate constants using quantum RRK theory fitted to these high-pressure results; the resulting microcanonical rate constants are then used in the computation of the pressure-dependent rate constants. Current implementations of SS-QRRK are for three types of reactions: unimolecular reactions (both isomerization, A P, and dissociation, A P1 + P2), bimolecular association reactions (A+B P), and bimolecular reaction with an associated intermediate and followed by a 2 nd step reaction(s) (A+B I product or products). Parallel reactions could be treated for certain type of reactions (see section 4). Unimolecular reactions (both unimolecular dissociation and unimolecular isomerization) are treated using Hinshelwood-Lindemann theory; bimolecular association reactions are treated with a chemical activation mechanism. 2.1 Hinshelwood Lindemann mechanism for unimolecular reactions Before we proceed to consider energy-resolved rate constants, we first examine the classical Lindemann mechanism for unimolecular reaction A P: Step 1: A + M k 1(T ) A + M k c (T ) Step 2: A k 2 (T ) P

5 In the original Lindemann model, the rate constants are assumed to be temperature-dependent and energy-independent. The thermal activation rate constant k 1 is modeled as: k 1 = Z exp( E 0 / k B T ) (1) where E 0 is called the threshold energy, k B is Boltzmann s constant, and Z is the bimolecular collision rate constant (in units of cm 3 molecule -1 s -1 ) between the reactant A and the bath gas M: Z = σ υ rel (2) where σ is a velocity-independent collision cross section between A and M, and υ rel is the average relative velocity. The rate constant k c of the de-activation step is simply equal to Z, which assumes that every collision of the energized molecule A* with M leads to de-energization (this is called the strong-collision assumption). The dissociation rate constant k 2 is simply the high-pressure-limit Arrhenius pre-exponential factor A uni. Using the steady-state approximation for A*, the unimolecular dissociation rate constant k uni (which is defined as 1 [A] In the high-pressure-limit ([M] >> 1), k uni d[a] ) is: dt k k uni = 1 [M] (3) 1+ k c [M] / k 2 = k1 k 2 / k c = A uni exp( E0 / k B T ) (4) and the unimolecular dissociation is a (pseudo-) first-order reaction; in the 0 low-pressure-limit ([M] 0), k uni order. = k 1 [M], and the dissociation reaction is of second As discussed next, our approach goes beyond the original theory mentioned above. In our approach, k uni(t ) is computed using VTST with multidimensional

6 tunneling; from now on, we will use canonical VTST (CVT) and small curvature tunneling (SCT) as an example of high-pressure-limit rate constants for our description in this manual (although in practice one may, for example, use other tunneling methods if desired). The threshold energy E 0 of the unimolecular dissociation reaction in SS-QRRK formalism is set equal to the temperature-dependent high-pressure-limit Arrhenius activation energy E a CVT/SCT (T ), which is computed as: E a = E(T 4 + 2T 0 T 3 2 T 0 T 2 ) (T 2 + nrt endothermic reaction 2 + T 0 ) 2 E(T 4 + 2T 0 T 3 T 0 2 T 2 ) (T 2 + T 0 2 ) 2 + nrt 2 T + T 0 exothermic reaction where E (kcal/mol) and T 0 (K) are fitting parameters in the following fitting formula for fitting the computed high-pressure-limit rate constants: (5) k = A( T 300 )n exp[ E(T + T 0 ) R(T 2 + T 0 2 ) ] A( T + T 0 300 )n exp[ E(T + T 0 ) R(T 2 + T 0 2 ) ] endothermic reaction exothermic reaction (6) and A uni(t ) is computed as A uni(t ) = kuni(t CVT/SCT )exp[ea (T ) / RT ] (7) The value of A uni(t ) is now temperature-dependent and we shall call it the frequency factor when it is used in SS-QRRK theory (see below). The energization and dissociation rate constants are treated as energy-dependent using SS-QRRK theory, and the collisional de-energization rate constant is computed based on modified strong collision model, which is discussed next. In particular, we consider the following thermal activation mechanism:

7 Step 1: A(T ) + M k 1(E; T ) A (E) + M k 2 (E) k c (T ) Step 2: A (E) P Step 1 is the thermal activation step, in which the thermally equilibrated unimolecular molecules (denoted as A(T) in the mechanism to denote that species A is at temperature T) collide with bath gas M to produce the rovibrationally excited reactant A * (E) with total rovibrational energy E randomized among all modes. The rate constant of thermal activation k 1 is a function of energy E and is parametrically dependent on T. The de-activation collisional rate constant k c is assumed to be temperature-dependent as in Lindemann Hinshelwood theory; it is computed as k c ( T ) = Zβ c (8) where Z is the Lennard-Jones collision rate constant, and β c is the collision efficiency. To model k 1 (E; T) and k 2 (E), we use single-frequency quantum Rice-Ramsperger-Kassel theory (QRRK), in which rotation is not treated explicitly, and the molecule consists of s identical oscillators with vibrational frequency ν, where we express ν in wave numbers (cm -1 ). In practice, we set s equal to number of vibrational degree of freedom (3N-6 for non-linear molecule), and ν is chosen to be the reactant geometric mean frequency. The geometric mean frequency is computed as: s v = ( v i ) 1/s (9) i=1 where ν i is the vibrational frequency of normal mode i, and s is the number of vibrational degrees of freedom. We denote the energy of the reactant molecule as E and set E equal to nhcν, where h is Planck's constant, c is the speed of light, and n is E/ hcν. In the QRRK model of the

8 microcanonical rate constant at energy E, a unimolecular reaction happens when a specific vibrational mode associated with the reaction coordinate possesses a critical energy (or threshold energy) E 0 equal to mhcν. Note that n and m are not usually integers. First consider k 1 (E;T). The equilibrium constant for step 1 is the fraction of the molecules with n quanta of excitation, which is K QRRK (n,t ) = exp( nhcν )[1 exp( hcν k B T k B T )]s (n + s 1)! n!(s 1)! (10) The equilibrium constant equals the ratio of forward to reverse rates: K QRRK (n,t ) = k 1 QRRK (E = nhcν;t ) / kc (T ) (11) Substituting Eq. (10) into Eq. (11) and solving for the forward rate yields k 1 QRRK (E;T ). Next consider the QRRK rate constant k 2 (E); this is equal to the frequency factor times the fraction of molecules with at least m quanta in one chosen mode, and for a quantum mechanical oscillator with s identical frequencies ν and temperature T, this is given by k 2 QRRK (E = nhcν ) = A QRRK n!(n m + s 1)! (n m)!(n + s 1)! (12) In SS-QRRK, we set the frequency factor A QRRK equal to A uni(t ) given by Eq. (7), and we set the threshold energy equal to the high-pressure local Arrhenius activation energy given by Eq. (5), which yields CVT/SCT m = E a (T ) / hcν (13) The analog of Eq. (3) is

9 k uni (T, p) = + QRRK k 1 (E = nhcν;t )[M] (14) k 1+ c (T )[M ] QRRK k 2 (E = nhcν ) n=m QRRK where k c ( T ) is obtained by Eq. (8), k 1 (E;T ) is obtained by Eqs. (10) and (11), and k 2 QRRK (E ) is from Eq (12). Now, it can be shown why we choose the frequency factor and threshold energy by Eqs. (7) and (5). In the high-pressure-limit, Eq. (14) reduces to: k uni (T, p) = + k 1 (E = nhcν;t )k 2 (E = nhcν ) (15) k c (T ) n=m and, by carrying out the summations, Eq. (4) is obtained. The high-pressure-limit canonical rate constants computed by SS-QRRK theory are therefore same as the ones determined by CVT/SCT theory. Therefore our SS-QRRK microcanonical rate constant formalism can build in variational effects, multidimensional tunneling based on the directly calculated potential energy surface along the tunneling path, and vibrational and torsional anharmonicity with no additional computational cost. 2.2 Chemical activation mechanism for bimolecular association The chemical activation mechanism for a bimolecular reaction with an associated intermediate is: A+B k1(t ) k 1(E) AB* kc[m] AB k 2(E) P (Type 1) and the chemical activation mechanism for a for bimolecular association reaction is:

10 A+B k1(t ) k 1(E) kc[m] AB* AB (Type 2) where A and B are reactants, AB* is the ro-vibrationally excited unimolecular state, AB is the stabilized unimolecular state (i.e., AB is the intermediate in a type-1 reaction, and it is the product of a type-2 reaction), and P is the product in a type-1 reaction. Applying the steady-state approximation to the chemical activation mechanism chemical activation mechanism yields + k stab = d[ab] [A][B]dt = k 1 MS-CVT/SCT k c [M] f (E) (16) QRRK k c [M]+ k 1 (E) + QRRK k2 (E) E 0 d[p] k P = [A][B]dt = k 1 MS-CVT/SCT + QRRK k 2 (E) f (E) (17) QRRK k c [M]+ k 1 (E) + QRRK k2 (E) for reaction type 1 and E 0 + k stab = d[ab] [A][B]dt = k 1 MS-CVT/SCT k c [M] f (E) (18) QRRK k c [M]+ k 1 (E) for reactions type 2, where f(e) is the fraction of energized species (AB*) at energy E, which is given by E 0 where f (E) = + E 0 k 1 QRRK (E)K(E) QRRK k 1 (E)K(E) K(E) = exp( nhv hv )[1 exp( k B T k B T )]s (n + s 1)! n!(s 1)! (19) (20) In eqs (16), (17), and (18), [M] is the concentration of the bath gas, which is calculated using the ideal gas law, [M] = p /RT, E 0 is the threshold energy, which is computed using Eq. (5), and k QRRK (E) denotes a quantum RRK theory energy-resolved rate constant, which is computed using Eq. (12) with the corresponding A factor and threshold energy.

11 The summations in eqs (16), (18), and (19) are evaluated with a step size of one quantum ( hv ). The quantity n! is computed using a gamma function or Stirling s approximation. 2.3 Energy transfer parameters The collision efficiency is computed by solving the following equation: β c 1 β c 1/2 = ΔE F E k B T (21) where ΔE (sometimes is also denoted as ΔE all, which is itself a negative number) is the average vibrational energy transferred during both energization and de energization processes (note that ΔE is smaller than the often encountered ΔE down parameter that is the average energy transferred in collisions in which the vibrational energy goes down); and F E is the thermal fraction of unimolecular states above the threshold energy and is defined in Troe s work (Troe, J. J. Chem. Phys. 1977, 66, 4745). For moderate sized molecules, F E is nearly unity (Troe, J. J. Phys. Chem. 1979, 83, 114). The temperature dependence of F E can be treated with Troe s method when it is needed: F E can be computed using Troe s definition: F E = + E 0 ρ(e)e E/k BT de k B T ρ(e 0 )e E 0 /k B T (22) or it can be computed using the Whiten-Rabinovitch approximation (J. Troe, J. Phys. Chem., 1979, 83, 114). Alternatively, it could be computed by using density of states come from multistructural coupled-torsional potential anharmonicity partition functions (MS-T); and this requires the usage of the MSTor program (which is a separate program that is freely downloadable from our group). The collision efficiency can also be estimated as:

12 β c = ΔE down ΔE down + F E k B T 2 (23) where ΔE down is the averaged energy transferred for only the de-activation process, by which we mean for only collisions in which the vibrational energy goes down. The Lennard-Jones collision rate constant k LJ is the product of the hard-sphere * collision rate constant k HS and the dimensionless reduced collision integral Ω 2,2, which is defined by Hirschfelder et al (Hirschfelder, J. O.; Curtiss, C. F.; Bird, R. B. In Molecular Theory of Gases and Liquids; Wiley and Sons: London, 1967.). Therefore * k c = β c Ω 2,2kHS (24) The values of the reduced collision integral can be evaluated by numerical integration and have been fitted by other workers with various simple algebraic expressions. Usually, we choose Troe s fitting expression (Troe, J. J. Chem. Phys. 1977, 66, 4745; Troe, J. J. * Chem. Phys. 1977, 66, 4758) for computing Ω 2,2 : * Ω 2,2 = [0.697 + 0.5185log 10 ( k B T ε A-M )] 1 [0.636 + 0.567log 10 ( k B T ε A-M )] 1 k B T ε A-M [3,300] k B T ε A-M [3,300] where ε A-M is the Lennard-Jones interaction parameter between molecule A and M and is computed as the geometric average of ε A-A and ε M-M. The hard sphere collision rate constant k HS is computed as: (25) k HS = π( d A + d M ) 2 8k B T 2 πµ (26) where the vdw diameters d A and d M are computed from the Lennard-Jones parameters σ A-A and σ M-M using the relation d = 2 1/6 σ, and µ is the reduced mass of A and M.

13 3. Fitting high-pressure-limit rate constants Before carrying out the SS-QRRK calculations, the user should use Polyrate to compute the high-pressure-limit rate constants and possibly to perform multi-structural torsional anharmonicity corrections using MSTor code. For transition states without conformational complexity one can use the original VTST, and for transition states with conformational complexity one can use multi-path or multi-structural VTST; in either case one can include multidimensional quantum mechanical tunneling. After computing the high-pressure-limit rate constants, the user should use the following equation to fit the rate constants (different formula should be applied for endothermic and exothermic reactions): k = A( T 300 )n exp[ E(T + T 0 ) R(T 2 + T 0 2 ) ] A( T + T 0 300 )n exp[ E(T + T 0 ) R(T 2 + T 0 2 ) ] endothermic reaction exothermic reaction (27) where A (for unimolecular reaction, its unit is s -1 ; and for bimolecular reaction, its unit is cm 3 molecule -1 s -1 ), n (unitless), E (unit: kcal/mol) and T 0 (unit: K) are fitting parameters. The ideal gas constant R is in the unit of kcal mol -1 K -1 with value 0.0019872. Then, the temperature-dependent Arrhenius activation energies can be computed from the local slopes of Arrhenius plots, which yields: E a = E(T 4 + 2T 0 T 3 2 T 0 T 2 ) (T 2 + nrt endothermic reaction 2 + T 0 ) 2 E(T 4 + 2T 0 T 3 T 0 2 T 2 ) (T 2 + T 0 2 ) 2 + nrt 2 T + T 0 exothermic reaction Finally, the local Arrhenius frequency factor A, which is also temperature-dependent, can be computed as: (28) A (T ) = k (T )exp[e a (T ) / RT ] (29)

14 4. Description of input The input of the SS-QRRK code is template-based; users should use the template that corresponds to their type of calculation and then change the values accordingly. Next we shall discuss the input templates for SS-QRRK calculations and the meanings of the keywords. Some common keywords are only explained once (in section 4.1). 4.1 Unimolecular reaction 4.1.1. Single Unimolecular reaction The input template for unimolecular reaction (A P) is: --------------------------------------------------------------------------------------------------------- #BasicInfo numbtrxn 10 Trxnlist 298. 300. 400. 500. 600. 700. 800. 900. 1000. 1500. numbp 11 unitp lg10bar Plist 3. 2.75 2.5 2.25 2. 1.75 1.5 1.25 1. 0.75-1.75 #Collision ColliIntg Troe avgetrans 740. cal*mol-1 0. all FE 1.15 parama 5.8 254.0 120.0 parambath 3.4 120.0 39.948 #FalloffMethod Method HLQRRK rxn1 AEa 9.405083E+10 24.3 1.006091E+11 24.4 4.716439E+11 25.4

15 6.669850E+11 25.7 7.699440E+11 25.9 8.789665E+11 26.1 1.013173E+12 26.2 1.167539E+12 26.5 1.361410E+12 26.7 2.658167E+12 28.5 sastar 30. GeoMeFreq 580.880669720707 MaxE 8000. #END Meanings of keywords: numbtrxn Trxnlist numbp unitp Plist ColliIntg avgetrans number of temperatures list of temperatures. This should be consistent with number of temperatures. number of pressures unit of the input pressures. Available options are: torr, bar, atm, Pa, kpa, lg10atm, lg10bar, lg10torr List of pressures; this should be consistent with number of pressures that user input The form of the collision integral one uses. Available options are: Troe, Reid Average energy transferred parameter ΔE. Available units are: cm**-1, kcal*mol-1, cal*mol-1. The temperature dependence can be incorporated by using: ΔE(T) =ΔE(T/300) n. There are two types of ΔE parameter: <ΔE> all (i.e. average energy transferred during both activation and deactivation collisions, which is specified by keyword all ), <ΔE> down (i.e., the average energy transferred only for deactivation collisions, which is specified by keyword down ). For example, avgetrans 740. cal*mol-1 0. all means we are using <ΔE> all = 740 cal/mol, and the temperature-dependence coefficient n = 0 (i.e., we do not consider T-dependence of <ΔE> all ).

16 FE The F E parameter for the activated unimolecular states. If the user specifies a positive number, then it means that the value specified by the user is directly used as F E ; if a value of -1 (negative one) is specified, then it means that F E will be computed based on Whitten-Rabinovitch approximation (with an additional input file: vibinfo.inp). Please refer to section 4.4 for more information about the additional input files. parama Lennard-Johns parameters for reactant A, in the order of σ (unit: Å), ε (unit: Kelvin, i.e., ε/k B ), molar mass (unit: gram per mole). parambath Method rxn1 AEa Lennard-Johns parameters for bath gas. For unimolecular dissociation or isomerization reaction, the keyword HLQRRK must be specified. To specify the A factor (temperature-dependent local frequency factor, which is determined by eq. (29)) and activation energy (determined by eq. (28), in the unit of kcal/mol) for the high-pressure-limit unimolecular reaction A P. Under this keyword, the user should specify A in left column and Ea in right column; this information should be consistent with the order of the temperatures that one has specified under Trxnlist sastar GeoMeFreq number of vibrational degree freedom of A The geometric mean frequency (in the unit of cm -1 ) of unimolecular reactant A. The geometric mean frequency is computed as eq. (9). MaxE The summation upper limit for quantum RRK theory (unit: kcal/mol); this value should be set to be high enough so that the summation is converged. A value of 8000 is recommended.

17 4.1.2 Unimolecular reaction with parallel reaction channels For the following thermal activation unimolecular reaction with multiple parallel reaction channels: A P1 P2! PN We give an example input file in below, for a unimolecular reaction with 3 parallel reaction channels: #BasicInfo numbtrxn 10 Trxnlist 298. 300. 400. 500. 600. 700. 800. 900. 1000. 1500. numbp 2 unitp lg10bar Plist 3. -1. #Collision ColliIntg Troe avgetrans 740. cal*mol-1 0. all FE -1 parama 5.8 254.0 120.0 parambath 3.4 120.0 39.948 #FalloffMethod Method PHLQRRK 3 rxn1 AEa 1 4.702541500E+10 24.3 5.030455000E+10 24.4 2.358219500E+11 25.4 3.334925000E+11 25.7 3.849720000E+11 25.9 4.394832500E+11 26.1 5.065865000E+11 26.2 5.837695000E+11 26.5 6.807050000E+11 26.7 1.329083500E+12 28.5 rxn1 AEa 2

18 4.702541500E+10 24.3 5.030455000E+10 24.4 2.358219500E+11 25.4 3.334925000E+11 25.7 3.849720000E+11 25.9 4.394832500E+11 26.1 5.065865000E+11 26.2 5.837695000E+11 26.5 6.807050000E+11 26.7 1.329083500E+12 28.5 rxn1 AEa 3 4.702541500E+10 24.3 5.030455000E+10 24.4 2.358219500E+11 25.4 3.334925000E+11 25.7 3.849720000E+11 25.9 4.394832500E+11 26.1 5.065865000E+11 26.2 5.837695000E+11 26.5 6.807050000E+11 26.7 1.329083500E+12 28.5 sastar 30. GeoMeFreq 580.880669720707 MaxE 4000. #END The key point in this input is that: (1) for a thermal activation unimolecular reaction with parallel channels, Method PHLQRRK 3 is required, in which PHLQRRK means we are applying Hinshelwood Lindemann SS-QRRK theory for parallel reactions ( P stands for parallel), and 3 means there are 3 parallel reaction channels (and the user should specify a number N if there are N parallel reactions instead of 3 parallel reactions that are used here as an example); (2) for each parallel reaction, the A and E a should be specified under the section rxn1 AEa I, where I represents the information for the I-th parallel reaction.

19 4.2 Bimolecular association The input template for bimolecular association reaction (A + B P) is as follows: #BasicInfo numbtrxn 3 Trxnlist 298.15 300. 400. numbp 4 unitp lg10atm Plist 3. -0.5-0.75-3. #Collision ColliIntg Troe avgetrans 92 cm**-1 0. all FE 1.15 parampstar 6.00 410.0 93.0 parambath 2.93 38.0 2.0 #FalloffMethod Method QRRK Rxn2 NO rxn1 rate 2.7165E-14 2.8101E-14 1.3146E-13 #QRRKData spstar 42. GeoMeFreq 1085.669208 MaxE 8000. rxnneg1aea 1.5444E+13 29.78 1.5961E+13 29.8 2.9953E+13 30.25 #END In section 4.1, we have already covered most common keywords. Here, we only explain new keywords: Method For bimolecular reactions, the keyword QRRK must be specified in order to do SS-QRRK calculation. (Do not be confused with the HLQRRK keyword, which is specifically used for unimolecular reaction with Hinshelwood-Lindemann theory.) Rxn2 NO For bimolecular association reaction, which does not involve a stable intermediate, the option for Rxn2 must be NO.

20 rxn1 rate User specified high-pressure-limit rate constant for the forward bimolecular association reaction (A + B P). rxnneg1aea To specify the A factor (temperature-dependent local frequency factor, which is determined by eq. (29)) and activation energy (determined by eq. (28), in the unit of kcal/mol) for the high-pressure-limit unimolecular reaction P A + B (i.e., the reverse reaction of bimolecular association). Under this keyword, the user should specify A in left column and Ea in right column; this information should be consistent with the order of the temperatures that one has specified under Trxnlist parampstar Lennard-Johns parameters for the unimolecular product P, in the order of σ (unit: Å), ε (unit: Kelvin, i.e., ε/k B ), molar mass (unit: gram per mole). spstar The number of vibrational degree of freedom for P. GeoMeFreq The geometric mean frequency (in the unit of cm -1 ) of unimolecular product P.

21 4.3 Bimolecular reaction with an intermediate 4.3.1 The input template for bimolecular reaction with a stable intermediate (A + B AB P) is: #BasicInfo numbtrxn 3 Trxnlist 298.15 300. 400. numbp 3 unitp lg10atm Plist 0.25 0. -0.25 #Collision ColliIntg Troe avgetrans 92 cm**-1 0. all FE 1.15 paramab 6.00 410.0 93.0 parambath 2.93 38.0 2.0 #FalloffMethod Method QRRK Rxn2 YES rxn1 rate 2.1632E-16 2.2860E-16 2.4896E-15 #QRRKData sabstar 42. GeoMeFreq 1092.49876 MaxE 8000. rxnneg1aea 1.7242E+12 26.55 1.9273E+12 26.61 4.3192E+13 28.62 rxn2aea 2.0228d+12 23.12 2.2603d+12 23.18 3.4447d+13 24.95 #END In section 4.1 and 4.2, we have already covered most common keywords. Here, we only explain new keywords: Method For bimolecular reactions with a stable intermediate, the keyword QRRK must be specified in order to do SS-QRRK calculation. (Do not be confused with the HLQRRK keyword, which is specifically

22 used for unimolecular reaction.) Rxn2 YES For bimolecular reactions with a stable intermediate, the Rxn2 must be set to be YES to indicate the existence of a second-step reaction. rxn2aea To specify the A factor (temperature-dependent local frequency factor, which is determined by eq. (29)) and activation energy (determined by eq. (28), in the unit of kcal/mol) for the high-pressure-limit unimolecular reaction AB P (i.e., the second-step reaction). Under this keyword, the user should specify A in left column and Ea in right column; this information should be consistent with the order of the temperatures that one has specified under Trxnlist rxnneg1aea To specify A factor and activation energy for high-pressure-limit reaction AB A + B rxn1 rate User specified high-pressure-limit rate constant for the forward bimolecular association reaction (A + B AB). GeoMeFreq paramab The geometric mean frequency (in the unit of cm -1 ) of unimolecular intermediate AB. Lennard-Johns parameters for the unimolecular intermediate AB, in the order of σ (unit: Å), ε (unit: Kelvin, i.e., ε/k B ), molar mass (unit: gram per mole). sabstar The number of vibrational degree of freedom for AB. 4.3.2. For a chemical activation mechanism that belongs to the following type: A + B AB P1 P2! PN

23 i.e., a bimolecular reaction with a stable intermediate being formed, and then followed by the second step consists of multiple parallel reactions (in the following example input, we have 3 parallel reactions in the second step; there is no limit in the number of parallel reactions that one can specify for the 2 nd step), the following input can be used: #BasicInfo numbtrxn 3 Trxnlist 298.15 300. 400. numbp 5 unitp lg10atm Plist 3. 0.25 0. -0.25-3. #Collision ColliIntg Troe avgetrans 92 cm**-1 0. all FE 1.15 paramab 6.00 410.0 93.0 parambath 2.93 38.0 2.0 #FalloffMethod Method QRRK Rxn2 3 rxn1 rate 2.1632E-16 2.2860E-16 2.4896E-15 #QRRKData sabstar 42. GeoMeFreq 1092.49876 MaxE 8000. rxnneg1aea 1.7242E+12 26.55 1.9273E+12 26.61 4.3192E+13 28.62 rxn2aea 1 1.0114d+12 23.12 1.13015d+12 23.18 1.72235d+13 24.95 rxn2aea 2 0.5057d+12 23.12 0.565075d+12 23.18 0.861175+13 24.95 rxn2aea 3 5.057d+11 21.12

24 5.65075d+11 21.18 8.61175+12 22.95 #END The key point in this input file is that, Rxn2 3 means there are 3 parallel reactions in the second step, and their A and E a parameters are specified respectively under the sections rxn2aea 1, rxn2aea 2, and rxn2aea 3, which are located after finishing specifying the information for the reverse reaction (from AB back to A + B) under the rxnneg1aea section. Also, please notice that Rxn2 1 is equivalent to Rxn2 YES, and Rxn2 0 is equivalent to Rxn2 NO in the previous section 4.2 and 4.3.

25 4.4 Other input files When the FE option is specified as -1, the F E factor is computed using the Whitten-Rabinovitch approximation. This is the most convenient option for computing F E. When the F E factor is computed by the Whitten-Rabinovitch approximation, vibinfo.inp is needed as additional input file. In vibinfo.inp, the vibrational zero-point energy (in kcal/mol, for the unimolecular species that is at the stationary point) is specified on the first line, followed by the vibrational frequencies (in cm -1 ). 39.76669 / ZPE in kcal/mol 67.6166 74.9266 81.1074 95.0748 114.2145 125.9215 321.9349 399.5684 410.5671 417.2896 438.9300 466.7933 543.3220 615.2602 665.2141 674.6209 860.1783 886.6351 926.5675 933.1321 934.0968 937.4362 1909.0212 2053.4916 2114.4137 2134.0820 2148.7552 2153.5027 2153.8935 2159.6340

26 5. Test runs We have included five test runs in Polyrate17/util/SS-QRRK/testrun/ and the corresponding output files are in Polyrate17/util/SS-QRRK/testo/ Test run1: Unimolecular reaction, with user specified F E =1.15 Test run2: Unimolecular reaction, with F E being computed by Whiten-Rabinovitch Test run3: Bimolecular reaction with an intermediate Test run4: Unimolecular reaction, with F E being computed from density of states Test run5: Bimolecular association reaction Test run6: Bimolecular reaction with an intermediate, and followed by the second step with 3 parallel reactions. Test run7: Unimolecular reaction with 3 parallel reaction channels.